MAST - Motif Alignment and Search Tool
MAST version 3.0 (Release date: 2001/03/01 11:41:04)
For further information on how to interpret these results or to get
a copy of the MAST software please access http://meme.sdsc.edu.
REFERENCE
If you use this program in your research, please cite:
Timothy L. Bailey and Michael Gribskov,
"Combining evidence using p-values: application to sequence homology
searches", Bioinformatics, 14(48-54), 1998.
DATABASE AND MOTIFS
DATABASE INO_up800.s (nucleotide)
Last updated on Thu Mar 1 08:28:30 2001
Database contains 7 sequences, 5600 residues
Scores for positive and reverse complement strands are combined.
MOTIFS meme.INO_up800.oops.4.sunsparcsolaris.html (nucleotide)
MOTIF WIDTH BEST POSSIBLE MATCH
----- ----- -------------------
1 12 TTCACATGCCGC
2 10 TCTGGCACAG
3 11 CAGCGGCACCA
PAIRWISE MOTIF CORRELATIONS:
MOTIF 1 2
----- ----- -----
2 0.32
3 0.16 0.44
No overly similar pairs (correlation > 0.60) found.
Random model letter frequencies (from non-redundant database):
A 0.281 C 0.222 G 0.229 T 0.267
SECTION I: HIGH-SCORING SEQUENCES
- Each of the following 7 sequences has E-value less than 10.
- The E-value of a sequence is the expected number of sequences
in a random database of the same size that would match the motifs as
well as the sequence does and is equal to the combined p-value of the
sequence times the number of sequences in the database.
- The combined p-value of a sequence measures the strength of the
match of the sequence to all the motifs and is calculated by
- finding the score of the single best match of each motif
to the sequence (best matches may overlap),
- calculating the sequence p-value of each score,
- forming the product of the p-values,
- taking the p-value of the product.
- The sequence p-value of a score is defined as the
probability of a random sequence of the same length containing
some match with as good or better a score.
- The score for the match of a position in a sequence to a motif
is computed by by summing the appropriate entry from each column of
the position-dependent scoring matrix that represents the motif.
- Sequences shorter than one or more of the motifs are skipped.
- The table is sorted by increasing E-value.
| Links | Sequence Name | Description | E-value | Length
|
|---|
|
| CHO2
| sequence of the region up...
| 1.1e-05
| 800
|
|
| INO1
| sequence of the region up...
| 1.6e-05
| 800
|
|
| ACC1
| sequence of the region up...
| 2.3e-05
| 800
|
|
| OPI3
| sequence of the region up...
| 3.1e-05
| 800
|
|
| FAS1
| sequence of the region up...
| 7.5e-05
| 800
|
|
| CHO1
| sequence of the region up...
| 9e-05
| 800
|
|
| FAS2
| sequence of the region up...
| 0.0012
| 800
|
SECTION II: MOTIF DIAGRAMS
- The ordering and spacing of all non-overlapping motif occurrences
are shown for each high-scoring sequence listed in Section I.
- A motif occurrence is defined as a position in the sequence whose
match to the motif has POSITION p-value less than 0.0001.
- The POSITION p-value of a match is the probability of
a single random subsequence of the length of the motif
scoring at least as well as the observed match.
- For each sequence, all motif occurrences are shown unless there
are overlaps. In that case, a motif occurrence is shown only if its
p-value is less than the product of the p-values of the other
(lower-numbered) motif occurrences that it overlaps.
- The table also shows the E-value of each sequence.
- Spacers and motif occurences are indicated by
- occurrence of motif `n' with p-value less than 0.0001.
A minus sign indicates that the occurrence is on the
reverse complement strand.
- Sequences longer than 1000 are not shown to scale and are indicated by thicker lines.
| Links | Name | Expect |    Motifs
|
|---|
|
| CHO2
| 1.1e-05
|
|
|
| INO1
| 1.6e-05
|
|
|
| ACC1
| 2.3e-05
|
|
|
| OPI3
| 3.1e-05
|
|
|
| FAS1
| 7.5e-05
|
|
|
| CHO1
| 9e-05
|
|
|
| FAS2
| 0.0012
|
|
| SCALE
|
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| 1
| 25
| 50
| 75
| 100
| 125
| 150
| 175
| 200
| 225
| 250
| 275
| 300
| 325
| 350
| 375
| 400
| 425
| 450
| 475
| 500
| 525
| 550
| 575
| 600
| 625
| 650
| 675
| 700
| 725
| 750
| 775
| 800
| |
|
|---|
SECTION III: ANNOTATED SEQUENCES
- The positions and p-values of the non-overlapping motif occurrences
are shown above the actual sequence for each of the high-scoring
sequences from Section I.
- A motif occurrence is defined as a position in the sequence whose
match to the motif has POSITION p-value less than 0.0001 as
defined in Section II.
- For each sequence, the first line specifies the name of the sequence.
- The second (and possibly more) lines give a description of the
sequence.
- Following the description line(s) is a line giving the length,
combined p-value, and E-value of the sequence as defined in Section I.
- The next line reproduces the motif diagram from Section II.
- The entire sequence is printed on the following lines.
- Motif occurrences are indicated directly above their positions in the
sequence on lines showing
- the motif number of the occurrence (a minus sign indicates that
the occurrence is on the reverse complement strand),
- the position p-value of the occurrence,
- the best possible match to the motif (or its reverse complement), and
- columns whose match to the motif has a positive score (indicated
by a plus sign).
CHO2
sequence of the region upstream from YGR157W
LENGTH = 800 COMBINED P-VALUE = 1.62e-06 E-VALUE = 1.1e-05
DIAGRAM: 27-[+3]-315-[+1]-47-[-2]-378
[+3]
1.4e-07
CAGCGGCACCA
+++++++++++
1 ACCCTCTAACGCGAATAAAGCGAATGACAGCGGCACCATTAATATGGCGAAACTGCAATTACTACCTGAAAACCA
[+1]
5.2e-07
TTCACATGCCGC
+++ ++++++++
301 ATATATATTTTTGCCTTGGTTTAAATTGGTCAAGACAGTCAATTGCCACACTTTTCTCATGCCGCATTCATTATT
[-2]
2.9e-05
CTGTGCCAGA
+ +++++++
376 CGCGAAGTTTTCCACACAAAACTGTGAAAATGAACGGCGATGCCAGAAACGGCAAAACCTCAAATGTTAGATAAC
INO1
sequence of the region upstream from YJL153C
LENGTH = 800 COMBINED P-VALUE = 2.35e-06 E-VALUE = 1.6e-05
DIAGRAM: 282-[-2]-78-[-3]-238-[-1]-55-[+1]-102
[-2]
1.8e-05
CTGTGCCAGA
+++ +++ ++
226 ACGTTGTATATGAAACGAGTAGTGAACGTTCGTACGATCTTTCACGCAGACATGCGACTGCGCCCGCCGTAGACC
[-3]
4.2e-
TGGTG
++++
301 GTGACCTGGAAGCTCACCCTGCAGAGGAATCTCAAGCACAGCCTCCAGCATATGATGAAGACGATGAGGCCGGTG
06
CCGCTG
++++++
376 CCGATGTGCCCTTGATGGACAACAAACAACAGCTCTCTTCCGGCCGTACTTAGTGATCGGAACGAGCTCTTTATC
[-1]
4.2e-08
GCGGCATGTGAA
++++++++++++
601 TGCGCTTCGGCGGCTAAATGCGGCATGTGAAAAGTATTGTCTATTTTATCTTCATCCTTCTTTCCCAGAATATTG
[+1]
1.3e-05
TTCACATGCCGC
+++++++++ ++
676 AACTTATTTAATTCACATGGAGCAGAGAAAGCGCACCTCTGCGTTGGCGGCAATGTTAATTTGAGACGTATATAA
ACC1
sequence of the region upstream from YNR016C
LENGTH = 800 COMBINED P-VALUE = 3.30e-06 E-VALUE = 2.3e-05
DIAGRAM: 82-[+1]-92-[+3]-34-[+2]-559
[+1]
3.1e-07
TTCACATGCCGC
++++++++++ +
76 TAAAATCTTCACATGGCCCGGCCGCGCGCGCGTTGTGCCAACAAGTCGCAGTCGAAATTCAACCGCTCATTGCCA
[+3]
2.1e-05
CAGCGGCACCA
++++++++++
151 CTCTCTCTACTGCTTGGTGAACTAGGCTATACGCTCAATCAGCGCCAAGATATATAAGAAGAACAGCACTCCCAG
[+2]
7.4e-07
TCTGGCACAG
++++++++++
226 TCGTATTCTGGCACAGTATAGCCTAGCACAATCACTGTCACAATTGTTATCGGTTCTACAATTGTTCTGCTCTCT
OPI3
sequence of the region upstream from YJR073C
LENGTH = 800 COMBINED P-VALUE = 4.45e-06 E-VALUE = 3.1e-05
DIAGRAM: 185-[-2]-144-[+1]-163-[-3]-275
[-2]
7.4e-07
CTGTGCCAGA
++++++++++
151 GTTAATCTGATCAACGCTACGCCGATGACAACGGTCTGTGCCAGATCTGGTTTTCCCCACTTATTTGCTACTTCC
[+1]
5.8e-06
TTCACATGCCGC
++++ ++ ++ +
301 AACTCCGTCAGGTCTTCCACGTGGAACTGCCAAGCCTCCTTCAGATCGCTCTTGTCGACCGTCTCCAAGAGATCC
[-3]
1.6e-06
TGGTGCCGCTG
+++++++++ +
451 TGTGTATCGGGGACTTCTCTTAGAGTAGAAGCGTCTATAAACCCAGGTGGGACGACAGTAGTGATGGCGCCGCCG
FAS1
sequence of the region upstream from YKL182W
LENGTH = 800 COMBINED P-VALUE = 1.08e-05 E-VALUE = 7.5e-05
DIAGRAM: 43-[+2]-41-[+1]-266-[+3]-417
[+2]
2.2e-05
TCTGGCACAG
++ +++++ +
1 CCGGGTTATAGCAGCGTCTGCTCCGCATCACGATACACGAGGTGCAGGCACGGTTCACTACTCCCCTGGCCTCCA
[+1]
4.2e-08
TTCACATGCCGC
++++++++++++
76 ACAAACGACGGCCAAAAACTTCACATGCCGCCCAGCCAAGCATAATTACGCAACAGCGATCTTTCCGTCGCACAA
[+3
2.0
CAG
+ +
301 TTTTGGCATTTTTGGCATACTTTTTATCGATTGAACCATCTTCTCCAAACACTTTTCCTTTTTCCTTCTATTCTG
]
e-05
CGGCACCA
+++ ++++
376 CAGGACCAACTAAAACTGGGTATATATATCATTATCTATATATATAAACGGCTTTCAACAAAGTTATAGGGGAAA
CHO1
sequence of the region upstream from YER026C
LENGTH = 800 COMBINED P-VALUE = 1.29e-05 E-VALUE = 9e-05
DIAGRAM: 38-[+3]-103-[+2]-396-[-2]-42-[+1]-17-[+1]-149
[+3]
3.5e-05
CAGCGGCACCA
+++++++ ++
1 CCGACCCAAATGTAATGGAACAATATTATTTGACACTTGATCAGCAGCAAAATAATCACCAAAATATGGCCTGGT
[+2]
3.9e-05
TCTGGCACAG
++++++ +
151 CGTCTGGCGCCCTTCCCATTCCGAACCATGTTATATTGAACCATCTGGCGACAAGCAGTATTAAGCATAATACAT
[-2]
7.4e-07
CTGTGCCAGA
++++++++++
526 CAATCCCCACTCCTTCTCAATGTGTGCAGACTTCTGTGCCAGACACTGAATATATATCAGTAATTGGTCAAAATC
[+1] [+1]
8.7e-07 2.2e-05
TTCACATGCCGC TTCACATGCCGC
++++++ +++ + +++++++++ +
601 ACTTTGAACGTTCACACGGCACCCTCACGCCTTTGAGCTTTCACATGGACCCATCTAAAGATGAAGATCCGTATT
FAS2
sequence of the region upstream from YPL231W
LENGTH = 800 COMBINED P-VALUE = 1.76e-04 E-VALUE = 0.0012
DIAGRAM: 184-[-2]-372-[+1]-194-[+3]-17
[-2]
2.9e-05
CTGTGCCAGA
++++++++
151 AACAGGGTGTCGGTCATACCGATAAAGCCGTCAAGAGTGCCAGAAAAGCAAGAAAGAACAAGATTAGATGTTGGT
[+1]
1.9e-06
TTCACATGCCGC
+++++++++ +
526 GCTTAGCAAAATCCAACCATTTTTTTTTTATCTCCCGCGTTTTCACATGCTACCTCATTCGCCTCGTAACGTTAC
[+3]
8.2e-06
CAGCGGCACCA
+++++ +++++
751 ATATTAGACGTTTAAAGGGCTACAGCAACACCAATTGAAATACCATCATT
Debugging Information
CPU: nbcr2
Time 0.080000 secs.
mast meme.INO_up800.oops.4.sunsparcsolaris.html -stdout
Button Help
Links to Entrez database at NCBI
Links to sequence scores (section I)
Links to motif diagrams (section II)
Links to sequence/motif annotated alignments (section III)
This information